As already pointed out, it depends on what you're trying to show / figure out.
But my generic advice would be to go with just C1' because the backbone can vary quite a bit even in more-or-less-B-form DNA. If you feel like getting a little fancier, add the atom on the other end of the glycosidic bond (note the atom number is different for pyrimidines vs. purines). The sublime thing about W:C pairing is that it keeps the orientation glycosidic bonds constant. ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu<mailto:pr...@uchicago.edu> http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Barry Finzel [finze...@umn.edu] Sent: Tuesday, January 22, 2013 9:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Superposing nucleic acids Minimally, I believe you want to use P and C1'. (This has been done by others, including Pabo and Pabo & Nekludova, J.Mol. Biol., 301:597-694 (2000). I actually prefer to use all backbone atoms: P O5' C5' C4' O3' C3' C2' C1' O1' Barry Finzel Medicinal Chemistry Department 2-160C Weaver-Densford Tel: (612) 626-5979 Lab: (612) 626-5226 Fax: (612) 624-0139 finze...@umn.edu<mailto:finze...@umn.edu> On Jan 22, 2013, at 9:00 AM, Alan Cheung wrote: Dear all - is there a convention for superposing nucleic acids duplexes of unrelated sequence? i.e. which atoms should be superposed : C4' of the sugar, P of the backbone, O3'/O5' of the backbone, or some combination thereof? Alan -- Alan Cheung Gene Center Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: che...@lmb.uni-muenchen.de<mailto:che...@lmb.uni-muenchen.de>
